RNA antibiotics
A Digital Approach to Novel RNA Antibiotics to fight diseases

Conventional antibiotics generally work against a broad spectrum of bacterial pathogens. This promotes the development of antibiotic resistance and damages our protective microbiota, which can have unwanted effects on our health. New antibiotics are therefore needed that can directly target individual pathogens, leaving beneficial bacteria unharmed. In a multidisciplinary approach, our team is researching antibiotics based on RNA-like molecules, so-called peptide nucleic acids (PNA), which can be used to specifically attack individual bacterial strains. These RNA antibiotics can be modified through simple chemical means to achieve effectiveness against emerging pathogens. In order to automate this process, we are creating a digital platform using high-throughput processes and machine learning, that will enable researchers to specifically design drug molecules against a variety of dangerous pathogens.

Strategy and conditions

Peptide nucleic acids are RNA-like molecules that bind to messenger RNA through complementary base pairing and can inhibit the production of proteins. This approach has already been confirmed to be effective in preclinical studies, but there are many open questions, for instance about the rules for programming such RNA antibiotics, mechanisms of resistance development, and possible toxicity to host cells and non-targeted members of the microbiome. We are pursuing a combination of transcriptome analysis and machine learning to understand the effects of PNAs on bacterial pathogens and to identify effective PNA candidates.

Aims of the research project

The goal of our research is to establish effective PNA candidates for important clinical pathogens. Towards this purpose, we will characterize the molecular basis of PNA activity and resistance development through the systematic analysis of high-throughput data. The knowledge we gain from these studies will form the basis for future logic design of RNA antibiotics to use against multi-drug resistant pathogens and editing the microbiome.

PNA coupling
Expected benefits for society

The development of programmable antibiotics will have major implications for the treatment of infection: as only the particular strain targeted is affected, issues of resistance development in other bacteria can be avoided. Additionally, this approach will avoid harming our natural commensal bacteria. This strategy could also be used to target specific functions of bacteria, for instance so that resistant bacteria become sensitive to conventional antibiotics, or pathogens no longer express toxins. Since certain bacterial pathogens are also associated with tumorigenesis, RNA antibiotics could also be of interest for cancer treatment or prophylaxis in the future.


Prof. Dr. Jörg Vogel
Project Management

Universität Würzburg
Medizinische Fakultät
Institut für Molekulare Infektionsbiologie

Jun. Prof. Dr. Franziska Faber
Project Management

Universität Würzburg
Medizinische Fakultät
Institut für Molekulare Infektionsbiologie

Jun. Prof. Dr. Lars Barquist
Project Management

Universität Würzburg
Medizinische Fakultät
Institut für Molekulare Infektionsbiologie

  • Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server
    Jakob Jung, Linda Popella, Phuong Thao Do, Patrick Pfau, Jörg Vogel, Lars Barquist
    RNA - A publication of the RNA Society 2023; 29: 570-583 ; McLean, Cold Spring Harbor Laboratory Press
  • INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors
    Jens Hör, Jakob Jung, Svetlana Ðurica-Mitić, Lars Barquist, Jörg Vogel
    Nucleic Acids Research 2022; 50(22): e128; Oxford, Oxford University Press
  • Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli
    Linda Popella, Jakob Jung, Phuong Thao Do, Regan J Hayward, Lars Barquist, Jörg Vogel
    Nucleic Acids Research 2022; 50(11): 6435–6452; Oxford, Oxford University Press
  • Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics
    Popella L, Jung J, Popova K, Durica-Mitić S, Barquist L, Vogel J
    Nucleic Acids Res 2021; 49(8): 4705-4724
  • An RNA biology perspective on species-specific programmable RNA antibiotics
    Jörg Vogel
    Mol Microbiol 2020; 113(3): 550-559
  • A decade of advances in transposon-insertion sequencing
    Cain AK, Barquist L, Goodman AL, Paulsen IT, Parkhill J
    Nat Rev Genet 2020; 9: 526-540
Associated Institutes

Julius-Maximilians-Universität Würzburg
Medizinische Fakultät
Institut für Molekulare Infektionsbiologie